Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions

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• 作者：Li Xiao ; Changhao Wang ; Xiang Ye ; Ray Luo
• 刊名：Journal of Physical Chemistry B
• 出版年：2016
• 出版时间：August 25, 2016
• 年：2016
• 卷：120
• 期：33
• 页码：8707-8721
• 全文大小：625K
• 年卷期：0
• ISSN：1520-5207

文摘

Continuum solvation modeling based upon the Poisson–Boltzmann equation (PBE) is widely used in structural and functional analysis of biomolecules. In this work, we propose a charge-central interpretation of the full nonlinear PBE electrostatic interactions. The validity of the charge-central view or simply charge view, as formulated as a vacuum Poisson equation with effective charges, was first demonstrated by reproducing both electrostatic potentials and energies from the original solvated full nonlinear PBE. There are at least two benefits when the charge-central framework is applied. First the convergence analyses show that the use of polarization charges allows a much faster converging numerical procedure for electrostatic energy and forces calculation for the full nonlinear PBE. Second, the formulation of the solvated electrostatic interactions as effective charges in vacuum allows scalable algorithms to be deployed for large biomolecular systems. Here, we exploited the charge-view interpretation and developed a particle–particle particle–mesh (P3M) strategy for the full nonlinear PBE systems. We also studied the accuracy and convergence of solvation forces with the charge-view and the P3M methods. It is interesting to note that the convergence of both the charge-view and the P3M methods is more rapid than the original full nonlinear PBE method. Given the developments and validations documented here, we are working to adapt the P3M treatment of the full nonlinear PBE model to molecular dynamics simulations.